[Pw_forum] PAW orthonormality and obtaining S|psi>
Hello all, I'm currently trying to use Quantum Espresso to generate the eigenfunctions for bulk and slab systems of PbS, which I then plan on projecting onto one another to determine the relative surface or bulk character of specific slab states. I've generated my sample systems and have run the scf/nscf calculations, but I've hit some trouble with the eigenvectors obtained from 'pw_export.x'. I have a couple questions that I hope some of you may be able to answer. Of course all my input files will be attached. To my surprise I found that different eigenstates of the same system are NOT orthonormal ( ~= 0.75, abs() ~= 0.15). I've done some searching and determined this may have to do with the PAW psuedo-potentials I am using. Is the PAW method the problem here? In trying to troubleshoot this, I found that eigenstate orthonormality may be obtained by including the 'uspp_spsi = .TRUE.' option in the 'pw_export.x' input file, which produces S|psi>, which is orthonormal by . Is this correct? If so, how can I project the two different systems on one another (bulk/slab), i.e. which system's eigenvector gets the 'S'? Finally (and sorry for all the questions at once), I've tried using the 'uspp_spsi = .TRUE.' option for both the bulk and slab systems, but I receive an error message for the bulk (but not the slab!): *** glibc detected *** pw_export.x: malloc(): memory corruption: 0x02b3a650 *** This occurs right as pw_export.x tries to produce the S|psi> files. I'm at a loss, and cannot proceed to troubleshoot this by myself any further. Does anyone have any insight into: (A) Whether I'm even taking the right approach, or (B) Why I could be getting this error for the bulk system but not the slab? Thank you all for your time, Hank Seeley University of Oregon, Chemistry Dept. &CONTROL calculation='nscf', outdir='./outdir/', prefix='PbS.111Pb_nlm127_scf', pseudo_dir='/ibrix/home6/hseeley/espresso-5.1.2/pseudo/', wf_collect = .true. , / &SYSTEM ibrav=0, celldm(1)=8.014979096, nat=24, ntyp=2, ecutwfc=40 , nbnd = 288 , noncolin = .true. , lspinorb = .true. , / &ELECTRONS / &IONS / &CELL / CELL_PARAMETERS {alat} 1.d0 0.d0 0.d0 -1.d0 1.732050807569d0 0.d0 0.d0 0.d0 9.79797900d0 ATOMIC_SPECIES Pb 207.20d0 Pb.rel-pbe-dn-kjpaw_psl.0.2.2.UPF S 32.065000d0 S.rel-pbe-n-kjpaw_psl.0.1.UPF ATOMIC_POSITIONS {alat} Pb -0.5 0.892231699 0.887974438 S0.0 0.601863122 1.194208995 S -0.5 1.413869605 1.229674758 Pb 0.5 0.285644600 1.640518112 Pb 0.0 1.169064255 1.611757402 S0.0 0.010823804 2.027962843 S -0.5 0.843840523 2.041869132 Pb 0.0 0.581181279 2.436519368 Pb -0.5 1.441040791 2.457622591 S0.5 0.288675135 2.857738033 S0.0 1.154700538 2.857738033 Pb 0.0 0.0 3.265986324 Pb -0.5 0.866025404 3.265986324 S0.0 0.577350269 3.674234614 S -0.5 1.443375673 3.674234614 Pb 0.5 0.284832308 4.095465222 Pb 0.0 1.157038022 4.074350526 S0.0 0.022183370 4.490167719 S -0.5 0.855209399 4.503996884 Pb 0.0 0.580385802 4.891465862 Pb -0.5 1.428998515 4.920233353 S0.5 0.264154080 5.337732348 S0.0 1.184230640 5.302306283 Pb 0.0 -0.026216765 5.643945872 K_POINTS {automatic} 1 1 1 0 0 0 &CONTROL title = 'PbS' , calculation = 'nscf' , outdir = './outdir/' , pseudo_dir = '/ibrix/home6/hseeley/espresso-5.1.2/pseudo/' , prefix = 'bulk_111PC' , wf_collect = .true. , verbosity = 'high' , / &SYSTEM ibrav=0, celldm(1)=8.014979096, nat=2, ntyp=2, ecutwfc=40 , noncolin = .true. , lspinorb = .true. , nbnd = 28 , / &ELECTRONS / &IONS / &CELL / CELL_PARAMETERS {alat} 1.d0 0.d0 0.d0 -0.5000d0 0.866025403784d0 0.d0 -0.5000d0 0.288675134595d0 0.816496580928d0 ATOMIC_SPECIES Pb 207.20d0 Pb.rel-pbe-dn-kjpaw_psl.0.2.2.UPF S 32.065000d0 S.rel-pbe-n-kjpaw_psl.0.1.UPF ATOMIC_POSITIONS {alat} S 0.00d0 0.5773502692d0 0.4082482905d0 Pb-0.50d0 0.2886751346d0 0.8164965809d0 K_POINTS {automatic} 1 1 1 0 0 0 &INPUTPP prefix = 'bulk_111PC' , outdir = './outdir/' , ascii = .true. , uspp_spsi = .true. , / ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] PAW orthonormality and obtaining S|psi>
Thank you Natalie, I've already used projwfc.x for these systems without the 'pawproj' option; I didn't realize I was doing this incorrectly! I'll definitely make this correction... I am still interested in obtaining the wavefunctions however. How do I go about getting the "correct" wavefunctions for the PAW method? Thank you again, Hank Seeley On 2016/04/16 07:21, Holzwarth, Natalie wrote: > Dear Henry, > In the PAW method, the atomic pseudo basis functions are not > designed to be orthogonal to each other, but there is a "dual > relationship" =\delta_{ij} with the projector > function p_i. One can use the projector function to estimate the > charge associated with an atomic site within the augmentation sphere > about that site. (Some notes are enclosed about this in case you are > interested. The main equations are correct, but the programming > details are no longer true.)Paolo Giannozzi programmed this into > quantum espresso in version 5.3.0.Perhaps this might suite your > needs?? In order to use it you need to use &projwfc: > > &projwfc > pawproj= .true. , << new option > outdir='$outd/', << old options; change as appropriate > prefix='$label', > filpdos='pdos', > Emin=-25.0, Emax=25.0, DeltaE=0.01, > ngauss=0, degauss=0.01 > / > > Sincerely, Natalie Holzwarth > > N. A. W. Holzwarth email: > nata...@wfu.edu > Department of Physics web: > http://www.wfu.edu/~natalie > Wake Forest University phone: > 1-336-758-5510 > Winston-Salem, NC 27109 USA office: Rm. 300 Olin > Physical Lab > > On Fri, Apr 15, 2016 at 8:02 PM, Henry J Seeley > wrote: > >> Hello all, >> >> I'm currently trying to use Quantum Espresso to generate the >> eigenfunctions for bulk and slab systems of PbS, which I then plan >> on projecting onto one another to determine the relative surface or >> bulk character of specific slab states. I've generated my sample >> systems and have run the scf/nscf calculations, but I've hit some >> trouble with the eigenvectors obtained from 'pw_export.x'. I have a >> couple questions that I hope some of you may be able to answer. Of >> course all my input files will be attached. >> >> To my surprise I found that different eigenstates of the same system >> are NOT orthonormal ( ~= 0.75, abs() ~= >> 0.15). I've done some searching and determined this may have to do >> with the PAW psuedo-potentials I am using. Is the PAW method the >> problem here? >> >> In trying to troubleshoot this, I found that eigenstate >> orthonormality may be obtained by including the 'uspp_spsi = .TRUE.' >> option in the 'pw_export.x' input file, which produces S|psi>, which >> is orthonormal by . Is this correct? If so, how can I >> project the two different systems on one another (bulk/slab), i.e. >> which system's eigenvector gets the 'S'? >> >> Finally (and sorry for all the questions at once), I've tried using >> the 'uspp_spsi = .TRUE.' option for both the bulk and slab systems, >> but I receive an error message for the bulk (but not the slab!): >> >> *** glibc detected *** pw_export.x: malloc(): memory corruption: >> 0x02b3a650 *** >> >> This occurs right as pw_export.x tries to produce the S|psi> files. >> I'm at a loss, and cannot proceed to troubleshoot this by myself any >> further. Does anyone have any insight into: >> (A) Whether I'm even taking the right approach, or (B) Why I could >> be getting this error for the bulk system but not the slab? >> >> Thank you all for your time, >> Hank Seeley >> University of Oregon, Chemistry Dept. >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] PAW orthonormality and obtaining S|psi>
On Sat, Apr 16, 2016 at 4:21 PM, Holzwarth, Natalie wrote: Paolo Giannozzi programmed this into quantum espresso in version 5.3.0. > I don't deserve that much credit: you programmed it, I just adapted it to v.5.3 Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] PAW orthonormality and obtaining S|psi>
Dear Henry, I don't know how to output the full PAW wavefunctions in quantum espresso. Did you want to evaluate ithem on a grid of real space points? There is a program called plotpaw.f90 that seems to output the full PAW density on a grid of points in real space.Is this close to what you want to do? In any case, I never used this program and the top says "experimental and incomplete program ...".Perhaps Paolo might clarify this?It could be that this existent code could be modified for your purposes?? Hopefully someone else might have a better answer. Sincerely, Natalie N. A. W. Holzwarth email: nata...@wfu.edu Department of Physics web: http://www.wfu.edu/~natalie Wake Forest University phone: 1-336-758-5510 Winston-Salem, NC 27109 USA office: Rm. 300 Olin Physical Lab On Sat, Apr 16, 2016 at 12:39 PM, Henry J Seeley wrote: > Thank you Natalie, > > I've already used projwfc.x for these systems without the 'pawproj' > option; I didn't realize I was doing this incorrectly! I'll definitely > make this correction... > I am still interested in obtaining the wavefunctions however. How do I > go about getting the "correct" wavefunctions for the PAW method? > > Thank you again, > Hank Seeley > > > On 2016/04/16 07:21, Holzwarth, Natalie wrote: > > Dear Henry, > > In the PAW method, the atomic pseudo basis functions are not > > designed to be orthogonal to each other, but there is a "dual > > relationship" =\delta_{ij} with the projector > > function p_i. One can use the projector function to estimate the > > charge associated with an atomic site within the augmentation sphere > > about that site. (Some notes are enclosed about this in case you are > > interested. The main equations are correct, but the programming > > details are no longer true.)Paolo Giannozzi programmed this into > > quantum espresso in version 5.3.0.Perhaps this might suite your > > needs?? In order to use it you need to use &projwfc: > > > > &projwfc > > pawproj= .true. , << new option > > outdir='$outd/', << old options; change as appropriate > > prefix='$label', > > filpdos='pdos', > > Emin=-25.0, Emax=25.0, DeltaE=0.01, > > ngauss=0, degauss=0.01 > > / > > > > Sincerely, Natalie Holzwarth > > > > N. A. W. Holzwarth email: > > nata...@wfu.edu > > Department of Physics web: > > http://www.wfu.edu/~natalie > > Wake Forest University phone: > > 1-336-758-5510 > > Winston-Salem, NC 27109 USA office: Rm. 300 Olin > > Physical Lab > > > > On Fri, Apr 15, 2016 at 8:02 PM, Henry J Seeley > > wrote: > > > >> Hello all, > >> > >> I'm currently trying to use Quantum Espresso to generate the > >> eigenfunctions for bulk and slab systems of PbS, which I then plan > >> on projecting onto one another to determine the relative surface or > >> bulk character of specific slab states. I've generated my sample > >> systems and have run the scf/nscf calculations, but I've hit some > >> trouble with the eigenvectors obtained from 'pw_export.x'. I have a > >> couple questions that I hope some of you may be able to answer. Of > >> course all my input files will be attached. > >> > >> To my surprise I found that different eigenstates of the same system > >> are NOT orthonormal ( ~= 0.75, abs() ~= > >> 0.15). I've done some searching and determined this may have to do > >> with the PAW psuedo-potentials I am using. Is the PAW method the > >> problem here? > >> > >> In trying to troubleshoot this, I found that eigenstate > >> orthonormality may be obtained by including the 'uspp_spsi = .TRUE.' > >> option in the 'pw_export.x' input file, which produces S|psi>, which > >> is orthonormal by . Is this correct? If so, how can I > >> project the two different systems on one another (bulk/slab), i.e. > >> which system's eigenvector gets the 'S'? > >> > >> Finally (and sorry for all the questions at once), I've tried using > >> the 'uspp_spsi = .TRUE.' option for both the bulk and slab systems, > >> but I receive an error message for the bulk (but not the slab!): > >> > >> *** glibc detected *** pw_export.x: malloc(): memory corruption: > >> 0x02b3a650 *** > >> > >> This occurs right as pw_export.x tries to produce the S|psi> files. > >> I'm at a loss, and cannot proceed to troubleshoot this by myself any > >> further. Does anyone have any insight into: > >> (A) Whether I'm even taking the right approach, or (B) Why I could > >> be getting this error for the bulk system but not the slab? > >> > >> Thank you all for your time, > >> Hank Seeley > >> University of Oregon, Chemistry Dept. > >> ___ > >> Pw_forum mailing list > >> Pw_forum@pwscf.org > >> http://pwscf.org/mailman/listinfo/pw_forum > > >
Re: [Pw_forum] PAW orthonormality and obtaining S|psi>
Thank you Natalie, I'll look into plotpaw, but I need to obtain the wavefunctions for specific states for my projections. -Hank Seeley On 2016/04/16 13:43, Holzwarth, Natalie wrote: > Dear Henry, >I don't know how to output the full PAW wavefunctions in > quantum espresso. Did you want to evaluate ithem on a grid of real > space points? There is a program called plotpaw.f90 that seems to > output the full PAW density on a grid of points in real space.Is > this close to what you want to do? In any case, I never used this > program and the top says "experimental and incomplete program ...". > Perhaps Paolo might clarify this?It could be that this existent > code could be modified for your purposes?? Hopefully someone else > might have a better answer. > Sincerely, Natalie > > N. A. W. Holzwarth email: > nata...@wfu.edu > Department of Physics web: > http://www.wfu.edu/~natalie > Wake Forest University phone: > 1-336-758-5510 > Winston-Salem, NC 27109 USA office: Rm. 300 Olin > Physical Lab > > On Sat, Apr 16, 2016 at 12:39 PM, Henry J Seeley > wrote: > >> Thank you Natalie, >> >> I've already used projwfc.x for these systems without the 'pawproj' >> option; I didn't realize I was doing this incorrectly! I'll >> definitely >> make this correction... >> I am still interested in obtaining the wavefunctions however. How do >> I >> go about getting the "correct" wavefunctions for the PAW method? >> >> Thank you again, >> Hank Seeley >> >> On 2016/04/16 07:21, Holzwarth, Natalie wrote: >>> Dear Henry, >>> In the PAW method, the atomic pseudo basis functions are not >>> designed to be orthogonal to each other, but there is a "dual >>> relationship" =\delta_{ij} with the projector >>> function p_i. One can use the projector function to estimate the >>> charge associated with an atomic site within the augmentation >> sphere >>> about that site. (Some notes are enclosed about this in case you >> are >>> interested. The main equations are correct, but the programming >>> details are no longer true.)Paolo Giannozzi programmed this >> into >>> quantum espresso in version 5.3.0.Perhaps this might suite >> your >>> needs?? In order to use it you need to use &projwfc: >>> >>> &projwfc >>> pawproj= .true. , << new option >>> outdir='$outd/', << old options; change as appropriate >>> prefix='$label', >>> filpdos='pdos', >>> Emin=-25.0, Emax=25.0, DeltaE=0.01, >>> ngauss=0, degauss=0.01 >>> / >>> >>> Sincerely, Natalie Holzwarth >>> >>> N. A. W. Holzwarth email: >>> nata...@wfu.edu >>> Department of Physics web: >>> http://www.wfu.edu/~natalie >>> Wake Forest University phone: >>> 1-336-758-5510 >>> Winston-Salem, NC 27109 USA office: Rm. 300 >> Olin >>> Physical Lab >>> >>> On Fri, Apr 15, 2016 at 8:02 PM, Henry J Seeley >> >>> wrote: >>> Hello all, I'm currently trying to use Quantum Espresso to generate the eigenfunctions for bulk and slab systems of PbS, which I then >> plan on projecting onto one another to determine the relative surface >> or bulk character of specific slab states. I've generated my sample systems and have run the scf/nscf calculations, but I've hit some trouble with the eigenvectors obtained from 'pw_export.x'. I have >> a couple questions that I hope some of you may be able to answer. >> Of course all my input files will be attached. To my surprise I found that different eigenstates of the same >> system are NOT orthonormal ( ~= 0.75, abs() ~= 0.15). I've done some searching and determined this may have to >> do with the PAW psuedo-potentials I am using. Is the PAW method the problem here? In trying to troubleshoot this, I found that eigenstate orthonormality may be obtained by including the 'uspp_spsi = >> .TRUE.' option in the 'pw_export.x' input file, which produces S|psi>, >> which is orthonormal by . Is this correct? If so, how >> can I project the two different systems on one another (bulk/slab), >> i.e. which system's eigenvector gets the 'S'? Finally (and sorry for all the questions at once), I've tried >> using the 'uspp_spsi = .TRUE.' option for both the bulk and slab >> systems, but I receive an error message for the bulk (but not the slab!): *** glibc detected *** pw_export.x: malloc(): memory corruption: 0x02b3a650 *** This occurs right as pw_export.x tries to produce the S|psi> >> files. I'm at a loss, and cannot proceed to troubleshoot this by myself >> any further. Does anyone have any insight into: (A) Whether I'm even taking the right approach, or (B) Why I >> could be getting this error f
Re: [Pw_forum] PAW orthonormality and obtaining S|psi>
On Sat, Apr 16, 2016 at 10:43 PM, Holzwarth, Natalie wrote: There is a program called plotpaw.f90 that seems to output the full PAW > density on a grid of points in real space.Is this close to what you > want to do? In any case, I never used this program and the top says > "experimental and incomplete program ...".Perhaps Paolo might clarify > this? > "experimental" because it is not thoroughly tested (but as far as I know it works), "incomplete" because it only computes the all-electron charge density on a line of points in real space. One might use code "pp.x" to plot the PAW charge density in 3D, but a very dense FFT grid is required to have a decent representation. Extending the codes to wavefunctions shouldn't be difficult but not straightforward either. On Sat, Apr 16, 2016 at 12:39 PM, Henry J Seeley wrote: I've already used projwfc.x for these systems without the 'pawproj' > option; I didn't realize I was doing this incorrectly! I do not think it is incorrect (or at least, I hope it isn't), it is just a different way to project Paolo ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] PAW orthonormality and obtaining S|psi>
I'm sorry to keep this thread alive so long but I'm confused. When I use 'pw_export.x' to obtain wavefunctions for my PAW system, what is it exactly that is being produced, if it is not the "full" wavefunction? Although these are not the "full" wavefunctions, could I still use them to compare the bulk and slab systems by manual projection between the two (via Matlab; I have my own code)? Modifying the existing 'pp.x' code to give only the wavefunctions sounds beyond my ability level; I am very unfamiliar with fortran. I appreciate the suggestion though, I would like to one day be able to add/modify some of the Quantum Espresso code for my own needs, but I don't see myself being able to do that for a long time (what you all do is very impressive). Thank you, Hank Seeley University of Oregon, Chemistry Department On 2016/04/17 23:54, Paolo Giannozzi wrote: > On Sat, Apr 16, 2016 at 10:43 PM, Holzwarth, Natalie > wrote: > >> There is a program called plotpaw.f90 that seems to output the full >> PAW density on a grid of points in real space.Is this close to >> what you want to do? In any case, I never used this program and >> the top says "experimental and incomplete program ...".Perhaps >> Paolo might clarify this? > > "experimental" because it is not thoroughly tested (but as far as I > know it works), "incomplete" because it only computes the all-electron > charge density on a line of points in real space. One might use code > "pp.x" to plot the PAW charge density in 3D, but a very dense FFT grid > is required to have a decent representation. Extending the codes to > wavefunctions shouldn't be difficult but not straightforward either. > > On Sat, Apr 16, 2016 at 12:39 PM, Henry J Seeley > wrote: > >> I've already used projwfc.x for these systems without the 'pawproj' >> option; I didn't realize I was doing this incorrectly! > > I do not think it is incorrect (or at least, I hope it isn't), it is > just a different way to project > > Paolo > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] PAW orthonormality and obtaining S|psi>
On Mon, Apr 18, 2016 at 5:59 PM, Henry J Seeley wrote: When I use 'pw_export.x' to obtain wavefunctions for my PAW system, what > is it exactly that is being produced, if it is not the "full" wavefunction? > presumably, the "smooth" part only, expanded into plane waves Although these are not the "full" wavefunctions, could I still use them > to compare the bulk and slab systems by manual projection between the > two maybe: the difference between the "full" and "smooth" wavefunctions should be relatively "atomic-like" > Modifying the existing 'pp.x' code to give only the wavefunctions sounds > beyond my ability level; I am very unfamiliar with fortran. fortran is the least of your problems. Really: fortran is trivial (especially compared to physics). Figuring out where are the quantities you need, and all the factors and units and other details that you have to know before you get the result right, is less trivial. Paolo > I appreciate the suggestion though, I would like to one day be able to > add/modify some of the Quantum Espresso code for my own needs, but I don't > see myself being able to do that for a long time (what you all do is very > impressive). > > Thank you, > Hank Seeley > University of Oregon, Chemistry Department > > On 2016/04/17 23:54, Paolo Giannozzi wrote: > > On Sat, Apr 16, 2016 at 10:43 PM, Holzwarth, Natalie > > wrote: > > > >> There is a program called plotpaw.f90 that seems to output the full > >> PAW density on a grid of points in real space.Is this close to > >> what you want to do? In any case, I never used this program and > >> the top says "experimental and incomplete program ...".Perhaps > >> Paolo might clarify this? > > > > "experimental" because it is not thoroughly tested (but as far as I > > know it works), "incomplete" because it only computes the all-electron > > charge density on a line of points in real space. One might use code > > "pp.x" to plot the PAW charge density in 3D, but a very dense FFT grid > > is required to have a decent representation. Extending the codes to > > wavefunctions shouldn't be difficult but not straightforward either. > > > > On Sat, Apr 16, 2016 at 12:39 PM, Henry J Seeley > > wrote: > > > >> I've already used projwfc.x for these systems without the 'pawproj' > >> option; I didn't realize I was doing this incorrectly! > > > > I do not think it is incorrect (or at least, I hope it isn't), it is > > just a different way to project > > > > Paolo > > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum